scPDB - 3d4b entry

Protein Data Bank Entry:

PDB ID : 3d4b

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent protein deacetylase
ID:	NPD_THEMA
AC:	Q9WYW0
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	29.982
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.296	752.625

% Hydrophobic	% Polar
54.71	45.29
According to VolSite

Ligand :

HET Code:	DZD
Formula:	C24H32N7O11P2
Molecular weight:	656.499 g/mol
DrugBank ID:	-
Buried Surface Area:	70.73 %
Polar Surface area:	305.4 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
8.49727	20.417	10.0563

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O36	N	ALA- 22	2.71	166.58	H-Bond (Protein Donor)	false
C31	CB	ALA- 22	3.88	0	Hydrophobic	false
C20	CB	ALA- 22	4.37	0	Hydrophobic	false
C62	CB	ALA- 22	3.84	0	Hydrophobic	false
N7	OG1	THR- 26	2.7	145.08	H-Bond (Protein Donor)	false
N10	OG1	THR- 26	3.31	138.02	H-Bond (Ligand Donor)	false
C63	CG2	ILE- 30	3.89	0	Hydrophobic	false
C20	CB	ASP- 32	4.14	0	Hydrophobic	false
C49	CE1	PHE- 33	4.33	0	Hydrophobic	false
C45	CD1	PHE- 33	3.87	0	Hydrophobic	false
C31	CB	PHE- 33	4.18	0	Hydrophobic	false
O33	N	PHE- 33	2.81	131	H-Bond (Protein Donor)	false
C63	CE	MET- 71	4.23	0	Hydrophobic	false
C38	CB	GLN- 98	4.24	0	Hydrophobic	false
O68	N	ILE- 100	2.9	154.38	H-Bond (Protein Donor)	false
C65	CG1	ILE- 100	4.22	0	Hydrophobic	false
N67	OD2	ASP- 101	2.69	161.23	H-Bond (Ligand Donor)	false
C49	CZ	PHE- 162	4.42	0	Hydrophobic	false
O37	OG	SER- 189	3.03	166.99	H-Bond (Protein Donor)	false
O37	N	SER- 190	2.68	153.25	H-Bond (Protein Donor)	false
O32	OG	SER- 190	2.75	158.96	H-Bond (Protein Donor)	false
C18	CB	SER- 190	4.14	0	Hydrophobic	false
C45	CG2	VAL- 193	3.53	0	Hydrophobic	false
O21	ND2	ASN- 214	3.23	164.28	H-Bond (Protein Donor)	false
N4	N	LEU- 215	3.06	166.28	H-Bond (Protein Donor)	false
O20	N	GLY- 216	3.2	141.81	H-Bond (Protein Donor)	false
N10	OD1	ASP- 231	2.67	128.86	H-Bond (Ligand Donor)	false
N6	N	VAL- 232	2.9	146.45	H-Bond (Protein Donor)	false